The purpose of this study was to examine the association between body mass index (BMI) and breast cancer intrinsic subtypes in Japanese women. A more complete understanding of the subtypes of breast cancer may elucidate the mechanisms affecting the etiology and mortality associated with each subtype. Tumor data on 531 invasive breast cancer cases subtyped by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (Her2) status were obtained [luminal A, luminal B, triple-negative (TN) and Her2-type]. Demographics (age at diagnosis, menopausal status and BMI) were collected from medical records. Case-only odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using logistic regression, adjusting for age at diagnosis. Of the 531 cases, 333 (62.7%) were luminal A, 85 (16.0%) were luminal B, 43 (8.1%) were Her2-type and 70 (13.2%) were TN. Compared with luminal A cases, premenopausal TN cases were more likely to be obese (OR, 4.11; 95% CI, 1.10–14.40), while postmenopausal TN cases were more likely to be underweight (OR, 3.14; 95% CI, 1.19–8.01). Premenopausal luminal B cases were likely to be underweight or obese, while luminal B and Her2-type cases were likely to be underweight. In the present study, significant heterogeneity of associations between BMI and tumor subtypes was observed. Breast cancer subtypes may have various etiologies associated with each subtype.